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Revision 1.4 - (view) (download) (as text)
| 1 : | olson | 1.1 | |
| 2 : | package FFserver; | ||
| 3 : | |||
| 4 : | use LWP::UserAgent; | ||
| 5 : | use Data::Dumper; | ||
| 6 : | olson | 1.3 | use YAML; |
| 7 : | olson | 1.1 | |
| 8 : | use strict; | ||
| 9 : | |||
| 10 : | sub new | ||
| 11 : | { | ||
| 12 : | my($class, $server_url) = @_; | ||
| 13 : | |||
| 14 : | olson | 1.3 | $server_url = "http://servers.nmpdr.org/figfam/server.cgi" unless $server_url; |
| 15 : | olson | 1.1 | |
| 16 : | |||
| 17 : | my $self = { | ||
| 18 : | server_url => $server_url, | ||
| 19 : | ua => LWP::UserAgent->new(), | ||
| 20 : | }; | ||
| 21 : | |||
| 22 : | return bless $self, $class; | ||
| 23 : | } | ||
| 24 : | |||
| 25 : | olson | 1.3 | sub members_of_families |
| 26 : | { | ||
| 27 : | my($self, @ids) = @_; | ||
| 28 : | olson | 1.4 | return $self->run_query('members_of_families', @ids); |
| 29 : | } | ||
| 30 : | |||
| 31 : | sub should_be_member | ||
| 32 : | { | ||
| 33 : | my($self, @id_seq_pairs) = @_; | ||
| 34 : | return $self->run_query('should_be_member', @id_seq_pairs); | ||
| 35 : | } | ||
| 36 : | |||
| 37 : | sub all_families | ||
| 38 : | { | ||
| 39 : | my($self) = @_; | ||
| 40 : | return $self->run_query('all_families'); | ||
| 41 : | } | ||
| 42 : | |||
| 43 : | sub run_query | ||
| 44 : | { | ||
| 45 : | my($self, $function, @args ) = @_; | ||
| 46 : | my $form = [function => $function, | ||
| 47 : | args => YAML::Dump(@args), | ||
| 48 : | ]; | ||
| 49 : | olson | 1.3 | return $self->run_query_form($form); |
| 50 : | } | ||
| 51 : | |||
| 52 : | sub run_query_form | ||
| 53 : | { | ||
| 54 : | my($self, $form) = @_; | ||
| 55 : | |||
| 56 : | my $res = $self->{ua}->post($self->{server_url}, $form); | ||
| 57 : | |||
| 58 : | if ($res->is_success) | ||
| 59 : | { | ||
| 60 : | return Load($res->content); | ||
| 61 : | } | ||
| 62 : | else | ||
| 63 : | { | ||
| 64 : | die "error on post " . $res->content; | ||
| 65 : | } | ||
| 66 : | } | ||
| 67 : | |||
| 68 : | olson | 1.1 | sub assign_function_to_prot |
| 69 : | { | ||
| 70 : | my($self, $input) = @_; | ||
| 71 : | |||
| 72 : | olson | 1.2 | my $wq; |
| 73 : | |||
| 74 : | olson | 1.1 | if (ref($input) eq 'ARRAY') |
| 75 : | { | ||
| 76 : | olson | 1.2 | $wq = SequenceListWorkQueue->new($input); |
| 77 : | olson | 1.1 | } |
| 78 : | else | ||
| 79 : | { | ||
| 80 : | olson | 1.2 | $wq = FastaWorkQueue->new($input); |
| 81 : | olson | 1.1 | } |
| 82 : | olson | 1.2 | |
| 83 : | return ResultHandler->new($wq, $self->{server_url}, 'assign_function_to_prot', \&id_seq_pair_bundler, \&tab_delimited_output_parser); | ||
| 84 : | olson | 1.1 | } |
| 85 : | |||
| 86 : | olson | 1.2 | sub assign_functions_to_dna |
| 87 : | olson | 1.1 | { |
| 88 : | olson | 1.2 | my($self, $input) = @_; |
| 89 : | olson | 1.1 | |
| 90 : | olson | 1.2 | my $wq; |
| 91 : | olson | 1.1 | |
| 92 : | olson | 1.2 | if (ref($input) eq 'ARRAY') |
| 93 : | olson | 1.1 | { |
| 94 : | olson | 1.2 | $wq = SequenceListWorkQueue->new($input); |
| 95 : | olson | 1.1 | } |
| 96 : | else | ||
| 97 : | { | ||
| 98 : | olson | 1.2 | $wq = FastaWorkQueue->new($input); |
| 99 : | olson | 1.1 | } |
| 100 : | olson | 1.2 | |
| 101 : | olson | 1.3 | return ResultHandler->new($wq, $self->{server_url}, 'assign_functions_to_DNA', \&id_seq_pair_bundler, \&tab_delimited_output_parser); |
| 102 : | olson | 1.2 | } |
| 103 : | |||
| 104 : | sub id_seq_pair_bundler | ||
| 105 : | { | ||
| 106 : | my($item) = @_; | ||
| 107 : | my($id, $seq) = @$item[0,2]; | ||
| 108 : | return "id_seq", join(",", $id, (ref($seq) eq 'SCALAR' ? $$seq : $seq)); | ||
| 109 : | } | ||
| 110 : | |||
| 111 : | sub tab_delimited_output_parser | ||
| 112 : | { | ||
| 113 : | my($line) = @_; | ||
| 114 : | chomp $line; | ||
| 115 : | my @cols = split(/\t/, $line); | ||
| 116 : | return \@cols; | ||
| 117 : | } | ||
| 118 : | |||
| 119 : | |||
| 120 : | sub tab_delimited_dna_data_output_parser | ||
| 121 : | { | ||
| 122 : | my($line) = @_; | ||
| 123 : | chomp $line; | ||
| 124 : | my ($id, $idbe, $fam) = split(/\t/, $line); | ||
| 125 : | my ($beg, $end) = $idbe =~ /_(\d+)_(\d+)$/; | ||
| 126 : | return [$id, $beg, $end, $fam]; | ||
| 127 : | olson | 1.1 | } |
| 128 : | |||
| 129 : | olson | 1.2 | package ResultHandler; |
| 130 : | olson | 1.1 | use strict; |
| 131 : | olson | 1.2 | use Data::Dumper; |
| 132 : | olson | 1.1 | |
| 133 : | sub new | ||
| 134 : | { | ||
| 135 : | olson | 1.2 | my($class, $work_queue, $server_url, $function, $input_bundler, $output_parser) = @_; |
| 136 : | |||
| 137 : | olson | 1.1 | my $self = { |
| 138 : | olson | 1.2 | work_queue => $work_queue, |
| 139 : | server_url => $server_url, | ||
| 140 : | function => $function, | ||
| 141 : | input_bundler => $input_bundler, | ||
| 142 : | output_parser => $output_parser, | ||
| 143 : | ua => LWP::UserAgent->new(), | ||
| 144 : | cur_result => undef, | ||
| 145 : | olson | 1.1 | }; |
| 146 : | return bless $self, $class; | ||
| 147 : | } | ||
| 148 : | |||
| 149 : | sub get_next | ||
| 150 : | { | ||
| 151 : | my($self) = @_; | ||
| 152 : | |||
| 153 : | olson | 1.2 | if ($self->{cur_result}) |
| 154 : | { | ||
| 155 : | return $self->get_next_from_result(); | ||
| 156 : | } | ||
| 157 : | else | ||
| 158 : | { | ||
| 159 : | my @inp = $self->{work_queue}->get_next_n_bytes(16000); | ||
| 160 : | if (@inp) | ||
| 161 : | { | ||
| 162 : | my $form = [function => $self->{function}, | ||
| 163 : | map { &{$self->{input_bundler}}($_) } @inp ]; | ||
| 164 : | # print "Invoke " .Dumper($form); | ||
| 165 : | |||
| 166 : | my $res = $self->{ua}->post($self->{server_url}, $form); | ||
| 167 : | if ($res->is_success) | ||
| 168 : | { | ||
| 169 : | $self->{cur_result} = $res->content; | ||
| 170 : | #print "res: $self->{cur_result}\n"; | ||
| 171 : | return $self->get_next_from_result(); | ||
| 172 : | } | ||
| 173 : | else | ||
| 174 : | { | ||
| 175 : | olson | 1.3 | die "error " . $res->status_line . " on post " . $res->content; |
| 176 : | olson | 1.2 | } |
| 177 : | } | ||
| 178 : | else | ||
| 179 : | { | ||
| 180 : | return; | ||
| 181 : | } | ||
| 182 : | } | ||
| 183 : | } | ||
| 184 : | |||
| 185 : | sub get_next_from_result | ||
| 186 : | { | ||
| 187 : | my($self) = @_; | ||
| 188 : | if ($self->{cur_result} =~ s/^([^\n]*)\n//) | ||
| 189 : | { | ||
| 190 : | return &{$self->{output_parser}}($1); | ||
| 191 : | } | ||
| 192 : | } | ||
| 193 : | |||
| 194 : | package SequenceWorkQueue; | ||
| 195 : | use strict; | ||
| 196 : | |||
| 197 : | sub new | ||
| 198 : | { | ||
| 199 : | my($class) = @_; | ||
| 200 : | |||
| 201 : | my $self = {}; | ||
| 202 : | |||
| 203 : | return bless $self, $class; | ||
| 204 : | } | ||
| 205 : | olson | 1.1 | |
| 206 : | olson | 1.2 | sub get_next_n |
| 207 : | { | ||
| 208 : | my($self, $n) = @_; | ||
| 209 : | my @out; | ||
| 210 : | |||
| 211 : | for (my $i = 0;$i < $n; $i++) | ||
| 212 : | olson | 1.1 | { |
| 213 : | olson | 1.2 | my($id, $com, $seqp) = $self->get_next(); |
| 214 : | if (defined($id)) | ||
| 215 : | { | ||
| 216 : | push(@out, [$id, $com, $seqp]); | ||
| 217 : | } | ||
| 218 : | else | ||
| 219 : | { | ||
| 220 : | last; | ||
| 221 : | } | ||
| 222 : | olson | 1.1 | } |
| 223 : | olson | 1.2 | return @out; |
| 224 : | } | ||
| 225 : | |||
| 226 : | sub get_next_n_bytes | ||
| 227 : | { | ||
| 228 : | my($self, $n) = @_; | ||
| 229 : | my @out; | ||
| 230 : | |||
| 231 : | my $size = 0; | ||
| 232 : | while ($size < $n) | ||
| 233 : | olson | 1.1 | { |
| 234 : | olson | 1.2 | my($id, $com, $seqp) = $self->get_next(); |
| 235 : | if (defined($id)) | ||
| 236 : | { | ||
| 237 : | push(@out, [$id, $com, $seqp]); | ||
| 238 : | $size += (ref($seqp) eq 'SCALAR') ? length($$seqp) : length($seqp); | ||
| 239 : | } | ||
| 240 : | else | ||
| 241 : | { | ||
| 242 : | last; | ||
| 243 : | } | ||
| 244 : | olson | 1.1 | } |
| 245 : | olson | 1.2 | return @out; |
| 246 : | olson | 1.1 | } |
| 247 : | |||
| 248 : | olson | 1.2 | package FastaWorkQueue; |
| 249 : | olson | 1.1 | use strict; |
| 250 : | olson | 1.2 | use base 'SequenceWorkQueue'; |
| 251 : | olson | 1.1 | use FileHandle; |
| 252 : | use FIG; | ||
| 253 : | |||
| 254 : | sub new | ||
| 255 : | { | ||
| 256 : | olson | 1.2 | my($class, $input) = @_; |
| 257 : | olson | 1.1 | |
| 258 : | my $fh; | ||
| 259 : | if (ref($input)) | ||
| 260 : | { | ||
| 261 : | $fh = $input; | ||
| 262 : | } | ||
| 263 : | else | ||
| 264 : | { | ||
| 265 : | $fh = new FileHandle("<$input"); | ||
| 266 : | } | ||
| 267 : | olson | 1.2 | |
| 268 : | my $self = $class->SUPER::new(); | ||
| 269 : | |||
| 270 : | $self->{fh} = $fh; | ||
| 271 : | |||
| 272 : | olson | 1.1 | return bless $self, $class; |
| 273 : | } | ||
| 274 : | |||
| 275 : | sub get_next | ||
| 276 : | { | ||
| 277 : | my($self) = @_; | ||
| 278 : | |||
| 279 : | olson | 1.2 | my($id, $seqp, $com) = &FIG::read_fasta_record($self->{fh}); |
| 280 : | return defined($id) ? ($id, $com, $seqp) : (); | ||
| 281 : | } | ||
| 282 : | |||
| 283 : | package SequenceListWorkQueue; | ||
| 284 : | use strict; | ||
| 285 : | use base 'SequenceWorkQueue'; | ||
| 286 : | olson | 1.1 | |
| 287 : | olson | 1.2 | sub new |
| 288 : | { | ||
| 289 : | my($class, $input) = @_; | ||
| 290 : | |||
| 291 : | my $fh; | ||
| 292 : | if (ref($input) ne 'ARRAY') | ||
| 293 : | olson | 1.1 | { |
| 294 : | olson | 1.2 | die "SequenceWorkQueue requires a list as input"; |
| 295 : | olson | 1.1 | } |
| 296 : | olson | 1.2 | |
| 297 : | my $self = $class->SUPER::new(); | ||
| 298 : | |||
| 299 : | $self->{list} = $input; | ||
| 300 : | |||
| 301 : | return bless $self, $class; | ||
| 302 : | } | ||
| 303 : | |||
| 304 : | sub get_next | ||
| 305 : | { | ||
| 306 : | my($self) = @_; | ||
| 307 : | |||
| 308 : | my $top = shift @{$self->{list}}; | ||
| 309 : | |||
| 310 : | return defined($top) ? @$top : (); | ||
| 311 : | olson | 1.1 | } |
| 312 : | olson | 1.2 | |
| 313 : | |||
| 314 : | olson | 1.1 | 1; |
| 315 : | olson | 1.2 |
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